From ESTs to ESRs

Comparative analysis of mutually exclusive exons in 15 species of insects

Patricia Buendia, Shu Ning Hsu, Akira Chiba, John Tyree, Robert Loredo

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequencing and microarrays. Exonic splicing regulatory sequences (ESRs) are cis-acting factor binding sites that regulate constitutive and alternative splicing. In this paper, we describe an in silico analysis pipeline to extract putative ESRs from EST splicing graphs and from a multiple alignment of 15 species of insects. Our method, E2E, combines graph analysis, phylogenetic measures and a sliding window approach that extracts conserved motifs using comparative analysis and the Welch's t statistic. We studied 100% conserved motifs as well as those obtained from our E2E method. We compared our results with a recent study on the alternatively spliced N-Cadherin gene in the Drosophila melanogaster. We also looked for homologous ESTs in mouse and human genome and found that about half of the putative ESRs in common between insects and mammals have a high statistical support (p<0.01).

Original languageEnglish
Title of host publication2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Pages46-51
Number of pages6
DOIs
StatePublished - Apr 14 2011
Event1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 - Orlando, FL, United States
Duration: Feb 3 2011Feb 5 2011

Other

Other1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
CountryUnited States
CityOrlando, FL
Period2/3/112/5/11

Fingerprint

Expressed Sequence Tags
Alternative Splicing
Paramagnetic resonance
Insects
Exons
Genes
Genome
Human Genome
Cadherins
Drosophila melanogaster
Computer Simulation
Mammals
Binding Sites
Technology
Binding sites
Microarrays
Pipelines
Throughput
Statistics

Keywords

  • Alternative splicing
  • Cis-acting
  • Comparative Analysis
  • ESRs
  • Motifs
  • Mutually exclusive exons
  • Regulatory elements
  • Sequence analysis
  • Splicing graphs

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Buendia, P., Hsu, S. N., Chiba, A., Tyree, J., & Loredo, R. (2011). From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects. In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 (pp. 46-51). [5729938] https://doi.org/10.1109/ICCABS.2011.5729938

From ESTs to ESRs : Comparative analysis of mutually exclusive exons in 15 species of insects. / Buendia, Patricia; Hsu, Shu Ning; Chiba, Akira; Tyree, John; Loredo, Robert.

2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011. 2011. p. 46-51 5729938.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Buendia, P, Hsu, SN, Chiba, A, Tyree, J & Loredo, R 2011, From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects. in 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011., 5729938, pp. 46-51, 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, United States, 2/3/11. https://doi.org/10.1109/ICCABS.2011.5729938
Buendia P, Hsu SN, Chiba A, Tyree J, Loredo R. From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects. In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011. 2011. p. 46-51. 5729938 https://doi.org/10.1109/ICCABS.2011.5729938
Buendia, Patricia ; Hsu, Shu Ning ; Chiba, Akira ; Tyree, John ; Loredo, Robert. / From ESTs to ESRs : Comparative analysis of mutually exclusive exons in 15 species of insects. 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011. 2011. pp. 46-51
@inproceedings{c731bb4a963e41d9b4a11bbd259dd14f,
title = "From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects",
abstract = "Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequencing and microarrays. Exonic splicing regulatory sequences (ESRs) are cis-acting factor binding sites that regulate constitutive and alternative splicing. In this paper, we describe an in silico analysis pipeline to extract putative ESRs from EST splicing graphs and from a multiple alignment of 15 species of insects. Our method, E2E, combines graph analysis, phylogenetic measures and a sliding window approach that extracts conserved motifs using comparative analysis and the Welch's t statistic. We studied 100{\%} conserved motifs as well as those obtained from our E2E method. We compared our results with a recent study on the alternatively spliced N-Cadherin gene in the Drosophila melanogaster. We also looked for homologous ESTs in mouse and human genome and found that about half of the putative ESRs in common between insects and mammals have a high statistical support (p<0.01).",
keywords = "Alternative splicing, Cis-acting, Comparative Analysis, ESRs, Motifs, Mutually exclusive exons, Regulatory elements, Sequence analysis, Splicing graphs",
author = "Patricia Buendia and Hsu, {Shu Ning} and Akira Chiba and John Tyree and Robert Loredo",
year = "2011",
month = "4",
day = "14",
doi = "10.1109/ICCABS.2011.5729938",
language = "English",
isbn = "9781612848525",
pages = "46--51",
booktitle = "2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011",

}

TY - GEN

T1 - From ESTs to ESRs

T2 - Comparative analysis of mutually exclusive exons in 15 species of insects

AU - Buendia, Patricia

AU - Hsu, Shu Ning

AU - Chiba, Akira

AU - Tyree, John

AU - Loredo, Robert

PY - 2011/4/14

Y1 - 2011/4/14

N2 - Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequencing and microarrays. Exonic splicing regulatory sequences (ESRs) are cis-acting factor binding sites that regulate constitutive and alternative splicing. In this paper, we describe an in silico analysis pipeline to extract putative ESRs from EST splicing graphs and from a multiple alignment of 15 species of insects. Our method, E2E, combines graph analysis, phylogenetic measures and a sliding window approach that extracts conserved motifs using comparative analysis and the Welch's t statistic. We studied 100% conserved motifs as well as those obtained from our E2E method. We compared our results with a recent study on the alternatively spliced N-Cadherin gene in the Drosophila melanogaster. We also looked for homologous ESTs in mouse and human genome and found that about half of the putative ESRs in common between insects and mammals have a high statistical support (p<0.01).

AB - Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequencing and microarrays. Exonic splicing regulatory sequences (ESRs) are cis-acting factor binding sites that regulate constitutive and alternative splicing. In this paper, we describe an in silico analysis pipeline to extract putative ESRs from EST splicing graphs and from a multiple alignment of 15 species of insects. Our method, E2E, combines graph analysis, phylogenetic measures and a sliding window approach that extracts conserved motifs using comparative analysis and the Welch's t statistic. We studied 100% conserved motifs as well as those obtained from our E2E method. We compared our results with a recent study on the alternatively spliced N-Cadherin gene in the Drosophila melanogaster. We also looked for homologous ESTs in mouse and human genome and found that about half of the putative ESRs in common between insects and mammals have a high statistical support (p<0.01).

KW - Alternative splicing

KW - Cis-acting

KW - Comparative Analysis

KW - ESRs

KW - Motifs

KW - Mutually exclusive exons

KW - Regulatory elements

KW - Sequence analysis

KW - Splicing graphs

UR - http://www.scopus.com/inward/record.url?scp=79953821108&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79953821108&partnerID=8YFLogxK

U2 - 10.1109/ICCABS.2011.5729938

DO - 10.1109/ICCABS.2011.5729938

M3 - Conference contribution

SN - 9781612848525

SP - 46

EP - 51

BT - 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

ER -